Molecular markers are the best method for investigating the genetic diversity. In this experiment, 72 cultivars including Indica and Japonica were investigated in Rice Research Centre of Iran. In order to evaluate the genetic diversity of locus waxy linked to the trait controlling the amylose content, PCR was performed using two oligonucleotides (484 and 485) and scored. The important Iranian cultivars of rice were screened using waxy microsatellite marker and classified into seven groups based on (CT)n repeats ranging from n=7 to 20. The amplified PCR products ranged from 102 to 128 bps in length and represented the (CT)n repeats of (CT)7, (CT)8, (CT)14, (CT)17, (CT)18, (CT)19 and (CT)20, that were according to amylose content of cultivars in Iranian germplasm classified in seven groups for that locus and explained 70%, 72%, 78.95%, 80% and 70% of each group variations, respectively.